VMD-L Mailing List

From: Prathit Chatterjee (pc20apr_at_REMOVE_yahoo.co.in)
Date: Sat Nov 07 2020 - 07:22:40 CST

 Dear VMD experts,
I had compiled a protein only amber trajectory of an explicitly solvated simulation with VMD, which I was able to visualize properly and run certain analyses with it in VMD as well.
But, for cross-checking, I tried to calculate the pairwise interaction of the original AMBER coordinates, and  the protein only generated trajectory (with VMD).
The results, although very similar, are showing certain discrepancy as follows:
[pchatterjee_at_node51 pairwise_IE]$ tail -f test*/pairwise_IE.out
==> test1/pairwise_IE.out <== [THIS IS THE ORIGINAL AMBER COORDINATE]
       1    -186.3642   -2973.0974
       2    -189.9812   -2966.1259
       3    -199.5370   -2957.7041
       4    -196.3846   -2983.7931
       5    -197.8264   -2981.1530
       6    -184.0711   -2971.6430
       7    -194.3659   -2970.1477
       8    -189.0441   -2956.9308
       9    -197.0864   -2948.2561
      10    -196.4939   -3010.1367

==> test2/pairwise_IE.out <==[THIS IS THE PROTEIN ONLY GENERATED AMBER COORIDNATE IN VMD]
       1    -186.3943   -2972.9815
       2    -189.9798   -2966.1573
       3    -199.5455   -2957.6502
       4    -196.3961   -2983.7881
       5    -197.8009   -2981.1609
       6    -184.0410   -2971.7176
       7    -194.3681   -2970.0830
       8    -189.0185   -2956.9181
       9    -197.1040   -2948.2302
      10    -196.4685   -3010.0947

Although the global picture will be the same with such minor discrepancy, I just want to know for the sake of knowing what the underlying reason could be.
Any comments/suggestions will be extremely helpful.
Thank you in advance,Best Regards,Prathit